ArticleiScience2020
Random Parametric Perturbations of Gene Regulatory Circuit Uncover State Transitions in Cell Cycle.
Article in iScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed, 25 citations in OpenAlex.
- Bacterial gene regulatory neural network as a biocomputing library of mathematical solvers.NPJ systems biology and applications · 2026Article
- Dissecting reversible and irreversible single cell state transitions from gene regulatory networks.Molecular systems biology · 2026Article
- sRACIPE 2.0: a systems biology circuit modeling toolkit for random circuit perturbation.Bioinformatics (Oxford, England) · 2026Article
- Building dynamical models of multi-step state transitions from single cell gene expression trajectories.bioRxiv : the preprint server for biology · 2025Article
- A computational approach for perturbation-induced EMT transitions.NPJ systems biology and applications · 2025Article
- Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML.NPJ systems biology and applications · 2024Article
- Constructing maps between distinct cell fates and parametric conditions by systematic perturbations.Bioinformatics (Oxford, England) · 2023Article
- Computational analysis of synergism in small networks with different logic.Journal of biological physics · 2023Article
- A quantitative evaluation of topological motifs and their coupling in gene circuit state distributions.iScience · 2023Article
- Article
- NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity.Genome biology · 2022Article
- What Makes a Functional Gene Regulatory Network? A Circuit Motif Analysis.The journal of physical chemistry. B · 2022Article
- Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits.Bioinformatics (Oxford, England) · 2021Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Many biological processes involve precise cellular state transitions controlled by complex gene regulation. Here, we use budding yeast cell cycle as a model system and explore how a gene regulatory circuit encodes essential information of state transitions. We present a generalized random circuit perturbation method for circuits containing heterogeneous regulation types and its usage to analyze both steady and oscillatory states from an ensemble of circuit models with random kinetic parameters. The stable steady states form robust clusters with a circular structure that are associated with cell cycle phases. This circular structure in the clusters is consistent with single-cell RNA sequencing data. The oscillatory states specify the irreversible state transitions along cell cycle progression. Furthermore, we identify possible mechanisms to understand the irreversible state transitions from the steady states. We expect this approach to be robust and generally applicable to unbiasedly predict dynamical transitions of a gene regulatory circuit.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.